enaDataGet download giving HTTP Error 400 error

[awitney]

enaDataGet is giving an error, is there a known issue?

$ enaDataGet NC_000962

Traceback (most recent call last):
  File "/homes/homedirs8/awitney/miniconda3/envs/data-download/bin/enaDataGet.py", line 89, in <module>
    elif not utils.is_available(accession):
  File "/homes/homedirs8/awitney/miniconda3/envs/data-download/bin/utils.py", line 240, in is_available
    response = urlrequest.urlopen(url)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 216, in urlopen
    return opener.open(url, data, timeout)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 525, in open
    response = meth(req, response)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 634, in http_response
    response = self.parent.error(
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 557, in error
    result = self._call_chain(*args)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 496, in _call_chain
    result = func(*args)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 749, in http_error_302
    return self.parent.open(new, timeout=req.timeout)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 525, in open
    response = meth(req, response)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 634, in http_response
    response = self.parent.error(
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 563, in error
    return self._call_chain(*args)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 496, in _call_chain
    result = func(*args)
  File "/homedirs8/awitney/miniconda3/envs/data-download/lib/python3.10/urllib/request.py", line 643, in http_error_default
    raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 400:
ERROR: Something unexpected went wrong please try again.
If problem persists, please contact [email protected] for assistance, with the above error details.

[blackadder901]

I am also experiencing the same issue.
I am trying to run the command both locally and in HPC but I am getting the same error.

[mweberr]

I have the same problem wondering what is the reason ?

[suranjayathilaka]

Hi! Could you please provide examples of the command that's failing?

[awitney]

This one is filing with the latest version

python enaBrowserTools-1.1.0/python3/enaDataGet.py ERR221663

although the error is now

urllib.error.URLError: <urlopen error [SSL: NO_CIPHERS_AVAILABLE] no ciphers available (_ssl.c:997)>

[Manishemblebi]

Hi @awitney ,
It seems like above error occurred due to handshake failure for SSL for python installed on client machine.
Please run the "Install Certificates.command" as suggested under readme and try again.

Also, please verify if below URL are accessible on the client machine -
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR221/ERR221663/ERR221663_1.fastq.gz

Thanks

[awitney]

Hi, just coming back to this as enaDataGet still not working for me. Isn't "Install Certificates.command" a command on a Mac installation? I am running centos. Yes i can access that file from the machine. Thanks

[cpaysan122]

I have the same problem wondering what is the reason ?

enaDataGet -f fastq SRX15831808

Command exit status:
1

Command output:
Checking availability of https://www.ebi.ac.uk/ena/browser/api/xml/SRX15831808

Command error:
Traceback (most recent call last):
File "/NetScratch/PLPOP/cpaysan/SRA_chlamydomonas_2024/bin/enaDataGet.py", line 116, in
readGet.download_files(accession, output_format, dest_dir, fetch_index, fetch_meta, aspera)
File "/NetScratch/PLPOP/cpaysan/SRA_chlamydomonas_2024/bin/readGet.py", line 93, in download_files
lines = utils.download_report_from_portal(search_url)
File "/NetScratch/PLPOP/cpaysan/SRA_chlamydomonas_2024/bin/utils.py", line 489, in download_report_from_portal
response = get_report_from_portal(url)
File "/NetScratch/PLPOP/cpaysan/SRA_chlamydomonas_2024/bin/utils.py", line 476, in get_report_from_portal
response = urlrequest.urlopen(request, context=gcontext)
File "/usr/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.7/urllib/request.py", line 531, in open
response = meth(req, response)
File "/usr/lib/python3.7/urllib/request.py", line 641, in http_response
'http', request, response, code, msg, hdrs)
File "/usr/lib/python3.7/urllib/request.py", line 569, in error
return self._call_chain(*args)
File "/usr/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/usr/lib/python3.7/urllib/request.py", line 649, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 400:
ERROR: Something unexpected went wrong please try again.
If problem persists, please contact ENA (https://www.ebi.ac.uk/ena/browser/support) for assistance, with the above error details.

[ctuni]

I'm also having the same issue with every accession that I try (the ones from the documentation themselves are failing as well).
Running enaBroserTool on an HPC cluster installed with easybuild, the error happens on both available versions of the tool (1.5.4 and 1.6).

[cpaysan122]

I used this tool instead : fastq-dl (https://github.com/rpetit3/fastq-dl) Christine Paysant - Le Roux Equipe Genomic Networks (Gnet) Paris-Saclay Institute of Plant Sciences (IPS2) UMR 1403 INRA-CNRS-UPSud-UP7-UEVE bâtiment 630 Plateau du moulon rue Noetzlin CS 80004 91192 GIF SUR YVETTE Cedex http://www.ips2.u-psud.fr bureau 1.82 (33) 1 69 15 75 89

…

________________________________ De : Cristina Tuñí i Domínguez ***@***.***> Envoyé : lundi 3 juin 2024 11:53:38 À : enasequence/enaBrowserTools Cc : Christine Paysant-Le-Roux; Comment Objet : Re: [enasequence/enaBrowserTools] enaDataGet download giving HTTP Error 400 error (Issue #66) I'm also having the same issue with every accession that I try (the ones from the documentation themselves are failing as well). Running enaBroserTool on an HPC cluster installed with easybuild, the error happens on both available versions of the tool (1.5.4 and 1.6). — Reply to this email directly, view it on GitHub<#66 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5WKI624HY6FWJYBAJSSSCLZFQVJFAVCNFSM5I246IWKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMJUGQ3DIOBQGI3A>. You are receiving this because you commented.Message ID: ***@***.***>

[ctuni]

I did not know about this other tool, it looks promising!
For anyone interested, I ended up using this other tool: https://github.com/enasequence/ena-ftp-downloader